[
https://issues.apache.org/jira/browse/JENA-1758?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16929236#comment-16929236
]
Andy Seaborne commented on JENA-1758:
-------------------------------------
[~dobrist]-- thank you for the excellent report and investigation.
The
[PR|https://github.com/apache/jena/pull/606|https://github.com/apache/jena/pull/606]
looks spot on.
The way to feed the loader with data that isn't from local file is
{{loader.stream()}} as your code has it. I hope you haven't had to make a
custom loader simply for that.
FYI: The variant of the loader that uses as much parallelism as possible can be
too aggressive and use all of the CPU cores and I/O bandwidth of the machine
that general OS scheduling is sluggish (minutes). This might impact a TCP
connection feeding a large amount of data, locking it out for long enough to
cause the TCP connection to drop out. I haven't seen this happen with the data
loader but from experience with other cases of machine saturation.
> Exception when preparing InfModel after TDB loading operation
> -------------------------------------------------------------
>
> Key: JENA-1758
> URL: https://issues.apache.org/jira/browse/JENA-1758
> Project: Apache Jena
> Issue Type: Bug
> Components: TDB2
> Affects Versions: Jena 3.12.0
> Reporter: Damien Obrist
> Assignee: Andy Seaborne
> Priority: Critical
> Fix For: Jena 3.13.0
>
> Time Spent: 20m
> Remaining Estimate: 0h
>
> h2. Exception
> I'm loading a few million triples into a TDB2 dataset. I'm using a custom
> loader (extending {{LoaderMain}}), since the triples being loaded are
> generated by a separate application and streamed in over HTTP.
> After the loading is done, I try to reset an {{InfModel}} to recompute the
> inference taking into account the new triples, but I encounter the following
> exception:
> {noformat}
> org.apache.jena.atlas.RuntimeIOException: Out of bounds: (limit
> 32834204)32834205
> at org.apache.jena.atlas.io.IO.exception(IO.java:254)
> at
> org.apache.jena.dboe.trans.data.TransBinaryDataFile.checkRead(TransBinaryDataFile.java:190)
> at
> org.apache.jena.dboe.trans.data.TransBinaryDataFile.read(TransBinaryDataFile.java:184)
> at
> org.apache.jena.tdb2.store.nodetable.TReadAppendFileTransport.read(TReadAppendFileTransport.java:71)
> at org.apache.thrift.transport.TTransport.readAll(TTransport.java:86)
> at
> org.apache.thrift.protocol.TCompactProtocol.readByte(TCompactProtocol.java:637)
> at
> org.apache.thrift.protocol.TCompactProtocol.readFieldBegin(TCompactProtocol.java:543)
> at
> org.apache.jena.riot.thrift.wire.RDF_IRI$RDF_IRIStandardScheme.read(RDF_IRI.java:318)
> at
> org.apache.jena.riot.thrift.wire.RDF_IRI$RDF_IRIStandardScheme.read(RDF_IRI.java:311)
> at org.apache.jena.riot.thrift.wire.RDF_IRI.read(RDF_IRI.java:258)
> at
> org.apache.jena.riot.thrift.wire.RDF_Term.standardSchemeReadValue(RDF_Term.java:319)
> at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:224)
> at org.apache.thrift.TUnion$TUnionStandardScheme.read(TUnion.java:213)
> at org.apache.thrift.TUnion.read(TUnion.java:138)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableTRDF.readNodeFromTable(NodeTableTRDF.java:80)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableNative._retrieveNodeByNodeId(NodeTableNative.java:103)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableNative.getNodeForNodeId(NodeTableNative.java:52)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableCache._retrieveNodeByNodeId(NodeTableCache.java:197)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableCache.getNodeForNodeId(NodeTableCache.java:108)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableWrapper.getNodeForNodeId(NodeTableWrapper.java:52)
> at
> org.apache.jena.tdb2.store.nodetable.NodeTableInline.getNodeForNodeId(NodeTableInline.java:66)
> at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:112)
> at org.apache.jena.tdb2.lib.TupleLib.quad(TupleLib.java:108)
> at
> org.apache.jena.tdb2.lib.TupleLib.lambda$convertToQuads$3(TupleLib.java:53)
> at org.apache.jena.atlas.iterator.Iter$2.next(Iter.java:270)
> at
> org.apache.jena.atlas.iterator.IteratorWrapper.next(IteratorWrapper.java:36)
> at
> org.apache.jena.tdb2.store.IteratorTxnTracker.next(IteratorTxnTracker.java:43)
> at
> java.util.Spliterators$IteratorSpliterator.tryAdvance(Spliterators.java:1812)
> at
> java.util.stream.StreamSpliterators$WrappingSpliterator.lambda$initPartialTraversalState$0(StreamSpliterators.java:294)
> at
> java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.fillBuffer(StreamSpliterators.java:206)
> at
> java.util.stream.StreamSpliterators$AbstractWrappingSpliterator.doAdvance(StreamSpliterators.java:169)
> at
> java.util.stream.StreamSpliterators$WrappingSpliterator.tryAdvance(StreamSpliterators.java:300)
> at java.util.Spliterators$1Adapter.hasNext(Spliterators.java:681)
> at org.apache.jena.atlas.iterator.Iter$2.hasNext(Iter.java:265)
> at org.apache.jena.atlas.iterator.Iter.hasNext(Iter.java:903)
> at org.apache.jena.atlas.iterator.Iter$1.hasNext(Iter.java:192)
> at
> org.apache.jena.util.iterator.WrappedIterator.hasNext(WrappedIterator.java:90)
> at
> org.apache.jena.reasoner.rulesys.impl.RETEEngine.fastInit(RETEEngine.java:155)
> at
> org.apache.jena.reasoner.rulesys.FBRuleInfGraph.prepare(FBRuleInfGraph.java:471)
> at
> org.apache.jena.rdf.model.impl.InfModelImpl.prepare(InfModelImpl.java:87)
> ...
> {noformat}
> h2. Code
> I tried to come up with a minimal example but wasn't able to reproduce the
> issue outside of my more involved application environment, where the issue
> occurs consistently. It seems to depend on a specific timing, the number of
> triples being loaded, the inference rules used etc.
> The code looks roughly like this:
> {code:java}
> // initialize
> Dataset dataset = TDB2Factory.connectDataset(path);
> Model unionModel = dataset.getNamedModel("urn:x-arq:UnionGraph");
> InfModel infModel = ModelFactory.createInfModel(reasoner, unionModel);
> Txn.executeRead(dataset, infModel::prepare);
> // load
> InputStream inputStream = // incoming HTTP stream
> DataLoader loader = new CustomLoader(LoaderPlans.loaderPlanParallel,
> dataset.asDatasetGraph);
> loader.startBulk();
> try {
> RDFDataMgr.parse(loader.stream(), inputStream, RDFLanguages.NQUADS);
> loader.finishBulk();
> } catch (RuntimeException e) {
> loader.finishException(e);
> throw e;
> }
> // reset model to recompute inference
> Txn.executeRead(dataset, () -> {
> model.reset();
> model.prepare();
> });
> {code}
--
This message was sent by Atlassian Jira
(v8.3.2#803003)
